The 1000 Genomes Project launched in 2008 with the goal of creating a public reference database for DNA polymorphism that is 95% complete at allele frequency 1%, and more complete for common variants and exonic variants, in each of multiple human population groups. The three pilot projects described here were designed to develop and evaluate methods to use high throughput sequencing to achieve these goals. The results indicate (a) that robust protocols now exist for generating both whole genome shotgun and targeted sequence data, (b) that algorithms to detect variants from each of these designs have been validated and (c) that low coverage sequencing offers an efficient approach to detect variation genome wide, whereas targeted sequencing offers an efficient approach to detect and accurately genotype rare variants in regions of functional interest (such as exons).
